Contacts of the helix formed by residues 92 - 119 (chain G) in PDB entry 1MFR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 92 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.6 19.6 - - - -
44G LEU* 3.8 8.0 - - - +
47G VAL* 4.1 17.0 - - + +
91G ASN* 1.3 72.1 - - - +
93G LEU* 1.3 58.3 + - - +
95G ALA* 3.6 1.2 + - - +
96G MET* 3.0 39.2 + - + +
151G LEU* 4.1 7.9 - - + -
156G LEU* 4.0 7.4 - - - -
163G GLU* 2.8 31.0 + - + +
166G PHE* 3.8 34.3 - - + -
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Residues in contact with LEU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G ASN* 2.9 10.5 + - - +
92G THR* 1.3 74.5 - - - +
94G GLU* 1.3 62.3 + - - +
96G MET* 3.3 1.6 + - - +
97G GLN* 2.9 52.4 + - + +
148G ILE* 3.9 30.3 - - + +
151G LEU* 3.9 24.2 - - + -
152G LYS* 4.3 16.2 - - + -
156G LEU* 3.4 18.2 - - + +
157G PRO* 3.7 36.1 - - + -
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Residues in contact with GLU 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ARG* 3.0 39.7 + - - +
89G TRP 3.4 12.3 - - - +
90G GLY* 3.7 7.9 - - - -
91G ASN* 3.1 27.3 + - - +
92G THR 3.4 0.2 - - - -
93G LEU* 1.3 79.2 - - - +
95G ALA* 1.3 57.1 + - - +
97G GLN* 3.5 14.6 + - - +
98G ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G MET* 3.8 9.8 - - - +
37G PHE* 3.7 27.1 - - + -
51G PHE* 4.1 11.7 - - + -
89G TRP* 3.7 16.1 + - + -
91G ASN 3.0 17.7 + - - +
92G THR 3.9 2.2 - - - +
94G GLU* 1.3 76.3 - - - +
96G MET* 1.3 60.2 + - - +
98G ALA* 3.4 8.1 + - - +
99G ALA* 2.9 27.7 + - - +
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Residues in contact with MET 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G VAL* 4.6 3.6 - - + -
50G PHE* 4.0 17.3 - - + -
51G PHE* 3.7 29.8 - - + -
92G THR* 3.0 27.2 + - + +
93G LEU 3.7 3.8 - - - +
95G ALA* 1.3 73.0 - - - +
97G GLN* 1.3 60.6 + - - +
99G ALA* 3.3 2.5 + - - +
100G LEU* 2.8 23.9 + - - +
144G ILE* 3.4 20.9 - - + +
147G PHE* 3.9 31.9 - - + -
148G ILE* 3.7 17.9 - - + +
151G LEU* 3.8 17.0 - - + -
166G PHE* 4.3 16.2 - - + -
171G VAL* 5.3 1.3 - - + -
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Residues in contact with GLN 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LEU* 2.9 41.8 + - + +
94G GLU* 3.8 14.5 - - - +
96G MET* 1.3 72.8 - - - +
98G ALA* 1.3 66.2 + - - +
100G LEU* 3.3 3.8 + - + +
101G GLN* 3.1 25.5 + - - +
148G ILE* 4.0 22.1 - - + +
152G LYS* 4.1 21.1 + - - -
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Residues in contact with ALA 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G MET* 4.0 4.7 - - + +
85G GLU* 5.4 4.0 - - - +
86G ARG* 5.6 2.2 - - - +
89G TRP* 3.8 32.5 - - + -
94G GLU 3.0 15.8 + - - +
95G ALA 3.5 8.5 - - - +
97G GLN* 1.3 75.4 - - - +
99G ALA* 1.3 56.6 + - - +
101G GLN* 3.4 7.1 + - - +
102G LEU* 3.0 28.1 + - - +
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Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G TYR* 3.9 27.8 + - + +
33G MET* 4.2 5.3 - - + +
51G PHE* 4.2 9.0 - - + -
95G ALA 2.9 17.7 + - - +
96G MET* 3.5 9.2 - - - +
98G ALA* 1.3 75.6 - - - +
100G LEU* 1.3 58.3 - - - +
102G LEU* 3.2 5.8 + - - +
103G GLU* 2.9 34.6 + - - +
144G ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F GLN* 3.8 38.6 - - + +
4F VAL* 4.9 0.4 - - + -
96G MET 2.8 19.3 + - - +
97G GLN* 3.3 6.9 + - - +
99G ALA* 1.3 72.8 - - - +
101G GLN* 1.3 58.5 + - + +
103G GLU* 3.4 3.6 + - - +
104G LYS* 3.0 42.1 + - + +
141G ILE* 3.9 42.2 - - + +
144G ILE* 3.9 11.6 - - + +
145G GLY* 4.5 3.4 - - - +
148G ILE* 3.7 23.1 - - + -
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Residues in contact with GLN 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G GLN 3.1 12.1 + - - +
98G ALA* 3.7 8.7 - - - +
99G ALA 3.3 0.2 - - - -
100G LEU* 1.3 75.8 - - + +
102G LEU* 1.3 61.0 + - - +
104G LYS* 3.2 10.2 + - - +
105G THR* 2.9 34.2 + - - +
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Residues in contact with LEU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 5.4 1.8 - - + -
25G TYR* 4.1 27.6 - - + -
26G ALA* 3.9 24.9 - - + +
29G THR* 3.7 28.0 - - + -
30G TYR* 3.9 33.2 - - + +
98G ALA 3.0 17.9 + - - +
99G ALA* 3.2 5.6 + - - +
101G GLN* 1.3 76.9 - - - +
103G GLU* 1.3 58.4 + - + +
105G THR* 3.4 10.2 + - + -
106G VAL* 3.1 35.7 + - + +
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Residues in contact with GLU 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G ALA* 6.5 0.4 - - - -
30G TYR* 2.8 29.1 + - - +
54G HIS* 3.6 14.4 + - - -
58G GLU* 3.4 13.2 - - - +
99G ALA 2.9 14.3 + - - +
100G LEU* 3.8 5.6 - - - +
102G LEU* 1.3 76.8 - - - +
104G LYS* 1.3 59.7 + - - +
106G VAL* 3.3 5.4 + - - +
107G ASN* 2.8 25.5 + - - +
137G GLN* 3.0 29.4 + - - +
140G ASP* 4.4 6.5 - - + -
141G ILE* 3.9 14.8 - - + -
144G ILE* 3.9 14.4 - - + -
177G MG 2.9 27.4 - - - -
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Residues in contact with LYS 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F SER 4.9 0.6 + - - -
3F GLN* 2.9 30.4 + - - +
4F VAL 4.4 5.6 - - - +
5F ARG 3.5 16.8 + - - -
6F GLN* 3.1 43.2 + - + +
100G LEU* 3.0 28.6 + - + +
101G GLN* 3.2 9.2 + - - +
103G GLU* 1.3 75.7 - - - +
105G THR* 1.3 55.6 + - - +
107G ASN* 4.1 0.4 - - - -
108G GLN* 2.9 26.0 + - - +
141G ILE* 4.2 11.7 - - + -
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Residues in contact with THR 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LEU* 4.6 19.3 - - + -
25G TYR* 6.5 0.4 - - + -
101G GLN* 2.9 21.5 + - - +
102G LEU* 3.5 12.7 - - + +
104G LYS* 1.3 76.6 - - - +
106G VAL* 1.3 63.7 + - - +
108G GLN* 3.4 6.5 + - - +
109G ALA* 3.1 22.2 + - - +
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Residues in contact with VAL 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G MET* 5.1 1.8 - - - -
22G LEU* 3.9 28.9 - - + +
23G GLU* 4.0 10.1 - - - +
26G ALA* 4.2 24.2 - - + -
58G GLU* 4.9 1.1 - - - +
102G LEU* 3.1 20.8 + - + +
103G GLU* 3.7 9.9 - - - +
105G THR* 1.3 72.4 - - - +
107G ASN* 1.3 66.4 + - - +
109G ALA* 3.2 2.8 + - - +
110G LEU* 3.0 30.8 + - + +
137G GLN* 3.9 11.7 - - - +
176G MG 3.8 22.2 - - - -
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Residues in contact with ASN 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLN* 3.1 39.9 + - - +
103G GLU 2.8 21.6 + - - +
104G LYS 3.6 0.2 - - - +
105G THR 3.3 0.2 - - - -
106G VAL* 1.3 72.6 - - - +
108G GLN* 1.3 58.0 + - - +
110G LEU* 3.1 10.3 + - - +
111G LEU* 2.9 41.7 + - - +
134G LEU* 4.8 9.0 - - - +
137G GLN* 3.6 21.9 - - - +
138G VAL* 5.0 10.3 - - - +
141G ILE* 3.9 16.9 - - + +
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Residues in contact with GLN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLN* 3.6 19.6 + - - +
7F ASN* 5.9 1.8 - - - +
104G LYS 2.9 18.2 + - - +
105G THR* 3.6 7.2 - - - +
107G ASN* 1.3 78.4 - - - +
109G ALA* 1.3 58.6 + - - +
111G LEU* 3.4 16.4 + - - +
112G ASP* 2.9 63.1 + - - +
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Residues in contact with ALA 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G MET* 3.1 20.0 - - + +
22G LEU* 3.7 21.8 - - + -
105G THR 3.1 14.1 + - - +
106G VAL 3.4 9.6 - - - +
108G GLN* 1.3 76.9 - - - +
110G LEU* 1.3 57.1 + - - +
112G ASP* 3.4 9.8 + - - +
113G LEU* 2.9 23.0 + - - +
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G MET* 3.7 24.5 - - + -
23G GLU* 4.9 1.3 - - - +
65G PHE* 4.0 20.9 - - + -
106G VAL* 3.0 25.5 + - + +
107G ASN* 3.1 6.7 + - - +
109G ALA* 1.3 74.7 - - - +
111G LEU* 1.3 61.6 + - - +
113G LEU* 3.4 3.4 + - + +
114G HIS* 2.9 26.3 + - - +
129G LEU* 4.2 15.0 - - + +
133G TYR* 3.9 31.4 - - + -
134G LEU* 3.9 15.2 - - + +
137G GLN* 3.7 31.0 - - + +
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Residues in contact with LEU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLN* 4.5 4.0 - - + -
7F ASN* 3.8 33.0 - - + +
123F PRO* 3.7 34.9 - - + +
124F HIS* 5.4 3.8 - - + +
107G ASN* 2.9 44.6 + - - +
108G GLN* 3.7 19.5 - - - +
109G ALA 3.3 0.2 - - - -
110G LEU* 1.3 74.4 - - - +
112G ASP* 1.3 60.4 + - - +
114G HIS* 3.2 6.7 + - - +
115G LYS* 3.0 26.7 + - - +
134G LEU* 4.6 16.6 - - + -
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Residues in contact with ASP 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G GLN* 2.9 48.0 + - - +
109G ALA* 3.4 9.7 - - - +
111G LEU* 1.3 76.3 - - - +
113G LEU* 1.3 60.4 + - - +
115G LYS* 3.3 8.6 + - - +
116G LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G CYS* 4.3 8.7 - - - +
15G ALA* 3.5 31.6 - - + +
16G VAL* 4.3 17.0 - - + -
19G MET* 3.7 34.8 - - + -
65G PHE* 4.5 2.2 - - + -
109G ALA 2.9 16.5 + - - +
110G LEU* 3.7 4.9 - - + +
111G LEU 3.3 0.2 - - - -
112G ASP* 1.3 75.8 - - - +
114G HIS* 1.3 58.7 + - - +
116G LEU* 3.4 10.8 + - + +
117G ALA* 3.0 26.7 + - - +
125G LEU* 4.4 9.6 - - + -
129G LEU* 3.9 25.8 - - + -
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Residues in contact with HIS 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F VAL* 6.1 1.4 - - - +
123F PRO* 3.5 36.4 - - + +
110G LEU 2.9 14.7 + - - +
111G LEU* 3.3 12.8 - - - +
112G ASP 3.1 0.2 - - - -
113G LEU* 1.3 76.0 - - - +
115G LYS* 1.3 61.8 + - - +
117G ALA* 3.3 4.2 + - - +
118G THR* 2.9 43.0 + - - -
126G CYS* 3.6 31.8 + - - +
129G LEU* 3.8 17.2 - - + +
130G GLU* 2.9 25.6 + - - -
134G LEU* 4.2 6.7 - - + -
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Residues in contact with LYS 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F VAL* 4.3 24.2 - - + -
111G LEU 3.0 12.7 + - - +
112G ASP* 3.3 11.4 + - - +
114G HIS* 1.3 74.5 + - - +
116G LEU* 1.3 61.2 + - - +
118G THR* 3.2 9.2 + - + +
119G ASP* 2.9 29.3 + - - +
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP* 3.6 39.9 - - + +
12G CYS* 4.0 11.9 - - - -
15G ALA* 3.7 19.7 - - + -
18G ARG* 5.4 2.5 - - - +
112G ASP 3.0 14.7 + - - +
113G LEU* 3.6 10.5 - - + +
114G HIS 3.3 0.2 - - - -
115G LYS* 1.3 76.2 - - - +
117G ALA* 1.3 56.6 + - - +
119G ASP* 3.3 6.4 + - + +
120G LYS* 2.9 50.2 + - + +
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Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G CYS* 4.3 11.2 - - - -
113G LEU 3.0 14.3 + - - +
114G HIS* 3.5 10.3 - - - +
116G LEU* 1.3 73.7 - - - +
118G THR* 1.3 63.8 + - - +
120G LYS 3.5 0.5 + - - -
121G VAL 3.1 3.6 + - - -
122G ASP* 2.9 34.1 + - + +
125G LEU* 3.9 28.3 - - + -
126G CYS* 3.6 17.5 - - - +
129G LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F VAL* 6.4 2.2 - - + -
114G HIS* 2.9 31.3 + - - -
115G LYS* 3.5 11.0 - - + +
117G ALA* 1.3 76.6 - - - +
119G ASP* 1.3 62.4 + - - +
121G VAL* 3.1 18.0 + - - +
126G CYS* 3.5 15.0 - - - -
----------------------------------------------------------
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Residues in contact with ASP 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G LYS 2.9 16.6 + - - +
116G LEU* 3.6 9.2 - - + +
118G THR* 1.3 77.3 - - - +
120G LYS* 1.3 72.5 + - + +
121G VAL* 3.2 9.2 + - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il